Add test case with estimated initial conditions specified via the con… (

#63) Add test case with estimated initial conditions specified via the conditions table Closes #62 Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
PEtab-dev · Jun 13, 2024 · 7c264b4 · 7c264b4
1 parent 2222464
commit 7c264b4
Show file tree

Hide file tree

Showing 26 changed files with 590 additions and 2 deletions.
diff --git a/petabtests/cases/v1.0.0/sbml/0011/0011.py b/petabtests/cases/v1.0.0/sbml/0011/0011.py
@@ -10,7 +10,7 @@
 
 This case tests initial concentrations in the condition table.
 For species `B`, the initial concentration is specified in the condition
-table, while for `A` it is given via an assignment rule in the SBML model.
+table, while for `A` it is given via an initial assignment in the SBML model.
 
 ## Model
 

diff --git a/petabtests/cases/v1.0.0/sbml/0011/README.md b/petabtests/cases/v1.0.0/sbml/0011/README.md
@@ -4,7 +4,7 @@
 
 This case tests initial concentrations in the condition table.
 For species `B`, the initial concentration is specified in the condition
-table, while for `A` it is given via an assignment rule in the SBML model.
+table, while for `A` it is given via an initial assignment in the SBML model.
 
 ## Model
 

diff --git a/petabtests/cases/v1.0.0/sbml/0019/0019.py b/petabtests/cases/v1.0.0/sbml/0019/0019.py
@@ -0,0 +1,69 @@
+from inspect import cleandoc
+
+import pandas as pd
+from petab.C import *
+
+from petabtests import PetabTestCase, analytical_a
+
+DESCRIPTION = cleandoc("""
+## Objective
+
+This case tests handling of initial concentrations that are specified
+in the conditions table. For species `A`, the initial concentration is
+estimated. For species `B`, the initial concentration is specified in the
+parameters table.
+
+## Model
+
+A simple conversion reaction `A <=> B` in a single compartment, following
+mass action kinetics.
+""")
+
+# problem --------------------------------------------------------------------
+
+condition_df = pd.DataFrame(data={
+    CONDITION_ID: ['c0'],
+    'A': ["initial_A"],
+    'B': ["initial_B"],
+}).set_index([CONDITION_ID])
+
+measurement_df = pd.DataFrame(data={
+    OBSERVABLE_ID: ['obs_a', 'obs_a'],
+    SIMULATION_CONDITION_ID: ['c0', 'c0'],
+    TIME: [0, 10],
+    MEASUREMENT: [0.7, 0.1]
+})
+
+observable_df = pd.DataFrame(data={
+    OBSERVABLE_ID: ['obs_a'],
+    OBSERVABLE_FORMULA: ['A'],
+    NOISE_FORMULA: [0.5]
+}).set_index([OBSERVABLE_ID])
+
+parameter_df = pd.DataFrame(data={
+    PARAMETER_ID: ['k1', 'k2', 'initial_A', 'initial_B'],
+    PARAMETER_SCALE: [LIN, LIN, LOG10, LIN],
+    LOWER_BOUND: [0, 0, 1, 0],
+    UPPER_BOUND: [10] * 4,
+    NOMINAL_VALUE: [0.8, 0.6, 2, 3],
+    ESTIMATE: [1] * 3 + [0],
+}).set_index(PARAMETER_ID)
+
+# solutions ------------------------------------------------------------------
+
+simulation_df = measurement_df.copy(deep=True).rename(
+    columns={MEASUREMENT: SIMULATION})
+simulation_df[SIMULATION] = [analytical_a(t, 2, 3, 0.8, 0.6)
+                             for t in simulation_df[TIME]]
+
+case = PetabTestCase(
+    id=19,
+    brief="Simulation. Estimated initial value via conditions table.",
+    description=DESCRIPTION,
+    model='conversion_modified.xml',
+    condition_dfs=[condition_df],
+    observable_dfs=[observable_df],
+    measurement_dfs=[measurement_df],
+    simulation_dfs=[simulation_df],
+    parameter_df=parameter_df,
+)
diff --git a/petabtests/cases/v1.0.0/sbml/0019/README.md b/petabtests/cases/v1.0.0/sbml/0019/README.md
@@ -0,0 +1,13 @@
+# PEtab test case 0019
+
+## Objective
+
+This case tests handling of initial concentrations that are specified
+in the conditions table. For species `A`, the initial concentration is
+estimated. For species `B`, the initial concentration is specified in the
+parameters table.
+
+## Model
+
+A simple conversion reaction `A <=> B` in a single compartment, following
+mass action kinetics.
diff --git a/petabtests/cases/v1.0.0/sbml/0019/_0019.yaml b/petabtests/cases/v1.0.0/sbml/0019/_0019.yaml
@@ -0,0 +1,11 @@
+format_version: 1
+parameter_file: _parameters.tsv
+problems:
+- condition_files:
+  - _conditions.tsv
+  measurement_files:
+  - _measurements.tsv
+  observable_files:
+  - _observables.tsv
+  sbml_files:
+  - _model.xml
diff --git a/petabtests/cases/v1.0.0/sbml/0019/_0019_solution.yaml b/petabtests/cases/v1.0.0/sbml/0019/_0019_solution.yaml
@@ -0,0 +1,7 @@
+chi2: 23.45305928312484
+llh: -12.17811234685187
+simulation_files:
+- _simulations.tsv
+tol_chi2: 0.001
+tol_llh: 0.001
+tol_simulations: 0.001
diff --git a/petabtests/cases/v1.0.0/sbml/0019/_conditions.tsv b/petabtests/cases/v1.0.0/sbml/0019/_conditions.tsv
@@ -0,0 +1,2 @@
+conditionId	A	B
+c0	initial_A	initial_B
diff --git a/petabtests/cases/v1.0.0/sbml/0019/_measurements.tsv b/petabtests/cases/v1.0.0/sbml/0019/_measurements.tsv
@@ -0,0 +1,3 @@
+observableId	simulationConditionId	time	measurement
+obs_a	c0	0	0.7
+obs_a	c0	10	0.1
diff --git a/petabtests/cases/v1.0.0/sbml/0019/_model.xml b/petabtests/cases/v1.0.0/sbml/0019/_model.xml
@@ -0,0 +1,87 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+  <model id="conversion_reaction_0" name="Conversion Reaction 0">
+
+    <listOfUnitDefinitions>
+      <unitDefinition id="volume" name="volume">
+        <listOfUnits>
+          <unit kind="litre" exponent="1" scale="-3" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="substance" name="substance">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+
+    <listOfCompartments>
+      <compartment id="compartment" name="compartment" spatialDimensions="3" size="1" constant="true">
+      </compartment>
+    </listOfCompartments>
+
+    <listOfSpecies>
+      <species id="A" name="A" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false">
+      </species>
+      <species id="B" name="B" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false">
+      </species>
+    </listOfSpecies>
+
+    <listOfParameters>
+      <parameter id="a0" name="a0" value="1" constant="true">
+      </parameter>
+      <parameter id="k1" name="k1" value="0" constant="true">
+      </parameter>
+      <parameter id="k2" name="k2" value="0" constant="true">
+      </parameter>
+    </listOfParameters>
+
+    <listOfInitialAssignments>
+      <initialAssignment symbol="A">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <ci> a0 </ci>
+        </math>
+      </initialAssignment>
+    </listOfInitialAssignments>
+
+    <listOfReactions>
+      <reaction id="fwd" name="fwd" reversible="false">
+        <listOfReactants>
+          <speciesReference species="A" stoichiometry="1"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="B" stoichiometry="1"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k1 </ci>
+              <ci> A </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction id="rev" name="rev" reversible="false">
+        <listOfReactants>
+          <speciesReference species="B" stoichiometry="1"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="A" stoichiometry="1"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k2 </ci>
+              <ci> B </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+
+  </model>
+</sbml>
diff --git a/petabtests/cases/v1.0.0/sbml/0019/_observables.tsv b/petabtests/cases/v1.0.0/sbml/0019/_observables.tsv
@@ -0,0 +1,2 @@
+observableId	observableFormula	noiseFormula
+obs_a	A	0.5
diff --git a/petabtests/cases/v1.0.0/sbml/0019/_parameters.tsv b/petabtests/cases/v1.0.0/sbml/0019/_parameters.tsv
@@ -0,0 +1,5 @@
+parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
+k1	lin	0	10	0.8	1
+k2	lin	0	10	0.6	1
+initial_A	log10	1	10	2.0	1
+initial_B	lin	0	10	3.0	0
diff --git a/petabtests/cases/v1.0.0/sbml/0019/_simulations.tsv b/petabtests/cases/v1.0.0/sbml/0019/_simulations.tsv
@@ -0,0 +1,3 @@
+observableId	simulationConditionId	time	simulation
+obs_a	c0	0	2.0
+obs_a	c0	10	2.1428570240673257
diff --git a/petabtests/cases/v1.0.0/sbml/0019/conversion_modified.xml b/petabtests/cases/v1.0.0/sbml/0019/conversion_modified.xml
@@ -0,0 +1,87 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+  <model id="conversion_reaction_0" name="Conversion Reaction 0">
+
+    <listOfUnitDefinitions>
+      <unitDefinition id="volume" name="volume">
+        <listOfUnits>
+          <unit kind="litre" exponent="1" scale="-3" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="substance" name="substance">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+
+    <listOfCompartments>
+      <compartment id="compartment" name="compartment" spatialDimensions="3" size="1" constant="true">
+      </compartment>
+    </listOfCompartments>
+
+    <listOfSpecies>
+      <species id="A" name="A" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false">
+      </species>
+      <species id="B" name="B" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false">
+      </species>
+    </listOfSpecies>
+
+    <listOfParameters>
+      <parameter id="a0" name="a0" value="1" constant="true">
+      </parameter>
+      <parameter id="k1" name="k1" value="0" constant="true">
+      </parameter>
+      <parameter id="k2" name="k2" value="0" constant="true">
+      </parameter>
+    </listOfParameters>
+
+    <listOfInitialAssignments>
+      <initialAssignment symbol="A">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <ci> a0 </ci>
+        </math>
+      </initialAssignment>
+    </listOfInitialAssignments>
+
+    <listOfReactions>
+      <reaction id="fwd" name="fwd" reversible="false">
+        <listOfReactants>
+          <speciesReference species="A" stoichiometry="1"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="B" stoichiometry="1"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k1 </ci>
+              <ci> A </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction id="rev" name="rev" reversible="false">
+        <listOfReactants>
+          <speciesReference species="B" stoichiometry="1"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="A" stoichiometry="1"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k2 </ci>
+              <ci> B </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+
+  </model>
+</sbml>
diff --git a/petabtests/cases/v1.0.0/sbml/README.md b/petabtests/cases/v1.0.0/sbml/README.md
@@ -70,3 +70,7 @@ Simulation. Preequilibration. One species reinitialized, one not (NaN in conditi
 
 Simulation. Preequilibration and RateRules. One state reinitialized, one not (NaN in condition table). InitialAssignment to species overridden.
 
+# [0019](0019/)
+
+Simulation. Estimated initial value via conditions table.
+
diff --git a/petabtests/cases/v2.0.0/sbml/0020/0020.py b/petabtests/cases/v2.0.0/sbml/0020/0020.py
@@ -0,0 +1,69 @@
+from inspect import cleandoc
+
+import pandas as pd
+from petab.C import *
+
+from petabtests import PetabTestCase, analytical_a
+
+DESCRIPTION = cleandoc("""
+## Objective
+
+This case tests handling of initial concentrations that are specified
+in the conditions table. For species `A`, the initial concentration is
+estimated. For species `B`, the initial concentration is specified in the
+parameters table.
+
+## Model
+
+A simple conversion reaction `A <=> B` in a single compartment, following
+mass action kinetics.
+""")
+
+# problem --------------------------------------------------------------------
+
+condition_df = pd.DataFrame(data={
+    CONDITION_ID: ['c0'],
+    'A': ["initial_A"],
+    'B': ["initial_B"],
+}).set_index([CONDITION_ID])
+
+measurement_df = pd.DataFrame(data={
+    OBSERVABLE_ID: ['obs_a', 'obs_a'],
+    SIMULATION_CONDITION_ID: ['c0', 'c0'],
+    TIME: [0, 10],
+    MEASUREMENT: [0.7, 0.1]
+})
+
+observable_df = pd.DataFrame(data={
+    OBSERVABLE_ID: ['obs_a'],
+    OBSERVABLE_FORMULA: ['A'],
+    NOISE_FORMULA: [0.5]
+}).set_index([OBSERVABLE_ID])
+
+parameter_df = pd.DataFrame(data={
+    PARAMETER_ID: ['k1', 'k2', 'initial_A', 'initial_B'],
+    PARAMETER_SCALE: [LIN, LIN, LOG10, LIN],
+    LOWER_BOUND: [0, 0, 1, 0],
+    UPPER_BOUND: [10] * 4,
+    NOMINAL_VALUE: [0.8, 0.6, 2, 3],
+    ESTIMATE: [1] * 3 + [0],
+}).set_index(PARAMETER_ID)
+
+# solutions ------------------------------------------------------------------
+
+simulation_df = measurement_df.copy(deep=True).rename(
+    columns={MEASUREMENT: SIMULATION})
+simulation_df[SIMULATION] = [analytical_a(t, 2, 3, 0.8, 0.6)
+                             for t in simulation_df[TIME]]
+
+case = PetabTestCase(
+    id=20,
+    brief="Simulation. Estimated initial value via conditions table.",
+    description=DESCRIPTION,
+    model='conversion_modified.xml',
+    condition_dfs=[condition_df],
+    observable_dfs=[observable_df],
+    measurement_dfs=[measurement_df],
+    simulation_dfs=[simulation_df],
+    parameter_df=parameter_df,
+)